OAuth Integration

Overview

BioContext7 supports OAuth 2.0 for accessing protected registries and APIs that require authenticated access.

Supported Providers

Provider	Protocol	Use Case
GitHub	OAuth 2.0	Private repository access
ORCID	OAuth 2.0	Researcher identity verification
GA4GH Passport	OAuth 2.0 + Visa	Controlled-access genomic data

GitHub OAuth

Configure

bc7 auth login github

This opens a browser for the OAuth flow. The token is stored securely in your system keychain.

Usage

Once authenticated, BioContext7 can access:

Private tool repositories
GitHub-hosted tool manifests
Repository metadata for tool verification

GA4GH Passport

For accessing controlled-access data through GA4GH Beacon and other federated services:

bc7 auth login ga4gh --issuer https://login.elixir-czech.org/oidc/

Visa Types

Visa	Description
`AffiliationAndRole`	Institutional affiliation
`AcceptedTermsAndPolicies`	Data use agreement acceptance
`ResearcherStatus`	Bona fide researcher status
`ControlledAccessGrants`	Specific dataset access grants

Token Management

# List stored tokens
bc7 auth list
 
# Remove a token
bc7 auth logout github
 
# Refresh an expired token
bc7 auth refresh github

Configuration

Override OAuth settings in ~/.biocontext7/config.yaml:

auth:
  github:
    client_id: "your-client-id"
    scopes: ["repo", "read:org"]
  ga4gh:
    issuer: "https://login.elixir-czech.org/oidc/"
    scopes: ["openid", "ga4gh_passport_v1"]

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